gplots protocols

gplots specifications

Information


Unique identifier OMICS_22070
Name gplots
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.0.1
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/gplots_3.0.1.tar.gz
Maintained Yes

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  • person_outline Gregory Warnes <>
  • person_outline Gregory Warnes <>

gplots IN pipelines

 (66)
2018
PMCID: 5761711
PMID: 29295970
DOI: 10.12659/MSM.905410

[…] of 2024 differentially expressed mrnas and 198 mirnas were identified by the “deseq” package in r. then, the heat map with complete linkage clustering of demrnas and demirnas was built using the “gplots” package in r. (supplementary figures 1, 2). as a result, there were 1042 (51.48%) up-regulated and 982 (48.52%) down-regulated degs. moreover, a total of 158 (79.79%) up-regulated and 40 […]

2018
PMCID: 5824801
PMID: 29476120
DOI: 10.1038/s41598-018-21992-9

[…] compared separately for brains and gonads, following the developers’ manual (false discovery rate, fdr, threshold of 0.05). principal component analysis (pca)153 and the heatmap.2 function in the gplots package154 were used to visualize global similarities and differences among either the brain or the gonadal samples. the global expression analysis conducted with sex and tissue […]

2018
PMCID: 5915011
PMID: 29455584
DOI: 10.1080/15548627.2017.1419118

[…] with the kegg pathway database (10.04.2016 download) [63-65]. the pathways with a benjamin-hochberg corrected p-value <0.005 are shown. the heatmap was generated using heatmap.2 function in gplots r package (http://cran.r-project.org/package=gplots)., raw264.7 cells were cultured in 25 mm hepes containing dmem or in dmem alone for 48h. secreted cytokine levels blotted and analyzed using […]

2018
PMCID: 5915011
PMID: 29455584
DOI: 10.1080/15548627.2017.1419118

[…] [63-65]. the pathways with a benjamin-hochberg corrected p-value <0.005 are shown. the heatmap was generated using heatmap.2 function in gplots r package (http://cran.r-project.org/package=gplots)., raw264.7 cells were cultured in 25 mm hepes containing dmem or in dmem alone for 48h. secreted cytokine levels blotted and analyzed using a mouse cytokine array panel a kit (r&d […]

2018
PMCID: 5919721
PMID: 29620157
DOI: 10.3892/ijo.2018.4336

[…] analysis. principal component analysis (regularized log-transformed, sizefactor-corrected counts obtained from deseq2), and data visualization were performed in r (version 3.4.0) using the packages gplots, ggfortify, genefilter and rcolorbrewer., based on the ngs data, differentially regulated cellular mirnas were validated by rt-qpcr. first, 111 ng of rna were reverse transcribed in triplicate […]

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